Evidence-Based Anatomy (EBA) is the concept of applying evidence-based principles and research methods to the anatomical sciences. While narrative reviews are common in the anatomical sciences, true systematic reviews (SR) and meta-analysis (MA) are only beginning to grow in popularity. In order to enhance the quality of future EBA studies, and ensure the clinical reliability of their results, a uniform methodology is needed. In this paper, we present a step-by-step methodological guide for performing SRs and MAs of anatomical studies. We address the EBA-specific challenges in each step of the SR and MA process, and discuss methods and strategies to overcome these difficulties. Furthermore, we discuss in detail the statistical methods used in MA of anatomical data, including multi-categorical and single-categorical pooled prevalence estimates, as well as pooled means of one group. Lastly, we discuss the major limitations of EBA, including the lack of a proper quality assessment tool for anatomical studies. The methods described in this paper present a uniform road map for future EBA studies.